Since the 1990s, many techniques for probing individual molecules have been developed. Below is a short summary of such techniques.
Fluorescence—many researchers use fluorescent labels specifically attached to molecules for tracking them by scanning techniques (e.g., confocal microscopy) or by observing them under a fluorescent microscope (e.g., using a microfluidic channel).
Raman spectroscopy—this is a method that gives chemical information about a molecule (i.e., a “molecular fingerprint”), but needs to be combined with plasmonic substrates for studying signals from single molecules (i.e., SERS: Surface Enhanced Raman Spectroscopy). These molecules need to be localized first by other methods (e.g., scanning techniques), immobilized, and the signal acquired for a long period of time.
High resolution microscopy—Scanning probe microscopes (e.g., Atomic Force Microscopes, Scanning Tunnel Microscopes, Near-field Scanning Optical Microscopes) or other high resolution microscopy techniques (e.g., Scanning Electron Microscopy, Transmission Electron Microscopy) can be used to study the topography of molecules or their mechanical properties. These techniques, however, may be destructive, slow, and give very little or no information that may be used to identify the molecules.
All of the above-listed techniques generally are slow and time consuming, use bulky equipment (e.g., optical or electronic microscopes, optical benches, etc.), all generally require complex sample preparation and scanning methods, and both the experiments and data interpretation need be carried out by one trained in the technique. Other drawbacks include the lack of throughput and poor versatility.